Enemy souls sometimes disappear, seed cannot be completed

[christopho]

When Shuffle Souls is set to "Bosses", all normal enemy souls are initially active. However, in some seeds, they sometimes disappear, making the seed impossible to complete.

This can be reproduced at least with the following seeds and steps:
https://ootrandomizer.com/seed/get?id=1927132
https://ootrandomizer.com/seed/get?id=1927140

• Create a new save file
• Start the game
• Pause the game
• Check the map screen : souls are there, as expected
• Reset the game without saving
• Restart the game
• Pause the game
• Check the map screen : souls are all gone

Video of these steps:
https://www.youtube.com/watch?v=4X2Bt72hoE8